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>>its funny because shes supposed to be ugly
Well she is not confirmed to be ugly by birth, just ungroomed, unclean, unhealthy looking, unconfident, shy and socially retarded. I am 99% certain that in the end of the story (if that will ever happen) she will look normal once she mans the fuck up, gets out of the isolation and starts to take care of herself. Really beauty is just so subtle and subjective.
And anyways this is a damned manga, here people are almost always idealized in looks, the author even makes note of that in story.